In the PolyExtrude SOP under the Extrude tab you can check Transform Extruded Front and change the Transform Space to Global. That will give you a plain world coordinate handle to extrude everything in a uniform direction.
If you find yourself doing this type of extrusion a lot you can set these values as permanent defaults: Click the gear icon at the top right of the PolyExtrude SOPs parameter pane and select Save As Permanent Defaults.

1) With Ryzen processors, memory speed can have an impact on render-times and overall CPU performance. Hard to say weather it's significant enough to spend extra money. I have a Threadripper with 3200MHz RAM, but I doubt it would be noticeably slower with 2933 or 3000. I think you're okay with 2400MHz and speed/capacity is something you can always upgrade down the line.
2) I would never get an AMD card for 3D work.
3) My Threadripper build was around $3,500, and still full of compromises. Have you considered the Threadripper 1900x though? I think it would be worth it to be on the X399 platform for upgrade-ability reasons. The mainstream Ryzen platforms limit you to only 64GB RAM and PCIe lanes/slots are limited.

I think the Noctua should do fine, especially if you're not overclocking.
We recently put together a Threadripper build at work using the 360 version of the Enermax. The chip is overclocked to 4GHz and under load it stays below 60C. That's pretty nice and quite a bit better than what the Corsair H115i in my system can do, it seems like the full-size cold plate makes a notable difference. Unfortunately the quality of the Enermax fans isn't so great as one of them is already making funny noises. They will probably have to get replaced with Noctua fans.

Hi, try just hitting Enter in the viewport (with the correct node selected). Does that bring the handle back? If not then maybe the handle display got turned off. Hold or right click the handle button and make sure the handle you want is checked. See attached image.

Basically what Sean said. Give the cup some thickness. In your cup Static Object, make sure you have an adequate collision representation. Uncheck Display Geometry and turn on the Collision Guide, and adjust the Division Size under Collisions > RBD Solver > Volume.
Once that looks good you'll want to make sure that the FLIP Object is creating adequate collision geometry from that. Turn on the Collision guide. To increase the resolution of the collision geometry created by the FLIP Object you can decrease Particle Separation, or enable Collision Separation and give it a value not tied to Particle Separation. Beyond that if you notice wonky behavior, like a few particles penetrating anyways, try increasing your substeps on the FLIP Solver. If trouble persists, please upload a file.

Hey Marty, CPU OpenCL does work on TR, it just wasn't as fast as the GPU. Unless you mean it's a suboptimal implementation.
It will use only one card. If you have something like GPU-Z installed you can choose which card to monitor, and during OpenCL only one of mine was under load.